-
Cellular and Molecular Biology... May 2024Plastic contamination can cause damage to the water quality of fish farm ponds, and also affect the quality of the final product. Pseudomonas mendocina was found to...
Plastic contamination can cause damage to the water quality of fish farm ponds, and also affect the quality of the final product. Pseudomonas mendocina was found to biodegrade plastics. Our study aimed to investigate the physicochemical properties and drug resistance of P. mendocina isolated from local freshwater aquaculture farms. Firstly, the strain was isolated from aquaculture water and then identified by matrix-assisted flight mass spectrometry and 16S rDNA sequencing. Then, biochemical and antibiotic resistance analyses were performed, and a microbial high-throughput growth detector was used to assess the growth of the strain. Finally, PCR and proteomics analyses were conducted to determine drug-resistance-related genes/proteins. According to the results of the spectrum diagram and sequencing, the isolated bacteria were identified as P. mendocina, and were positive for reactions of ADH, MTE, LAC, MNE, FRU, CIT, MLT, ONPG, and ACE. P. mendocina was sensitive to most of the antibiotics, and its resistance to CHL, MIN, and TIC/CLA was intermediate. Additionally, gyrB was the resistance gene, and mdtA2, mdtA3, mdaB, and emrK1 were closely related to the drug resistance of P. mendocina. Our results show the biochemical properties of P. mendocina in isolated aquaculture water, and provide a new perspective for P. mendocina involved in the biological removal of plastics or microplastics in freshwater aquaculture farms.
Topics: Aquaculture; Fresh Water; Pseudomonas mendocina; RNA, Ribosomal, 16S; Anti-Bacterial Agents; Phylogeny; Farms; Microbial Sensitivity Tests; Bacterial Proteins; Drug Resistance, Bacterial; Animals
PubMed: 38814239
DOI: 10.14715/cmb/2024.70.5.4 -
Molecular Biology Reports May 2024
PubMed: 38704763
DOI: 10.1007/s11033-024-09536-z -
PLoS Genetics Mar 2024C. elegans can learn to avoid pathogenic bacteria through several mechanisms, including bacterial small RNA-induced learned avoidance behavior, which can be inherited...
C. elegans can learn to avoid pathogenic bacteria through several mechanisms, including bacterial small RNA-induced learned avoidance behavior, which can be inherited transgenerationally. Previously, we discovered that a small RNA from a clinical isolate of Pseudomonas aeruginosa, PA14, induces learned avoidance and transgenerational inheritance of that avoidance in C. elegans. Pseudomonas aeruginosa is an important human pathogen, and there are other Pseudomonads in C. elegans' natural habitat, but it is unclear whether C. elegans ever encounters PA14-like bacteria in the wild. Thus, it is not known if small RNAs from bacteria found in C. elegans' natural habitat can also regulate host behavior and produce heritable behavioral effects. Here we screened a set of wild habitat bacteria, and found that a pathogenic Pseudomonas vranovensis strain isolated from the C. elegans microbiota, GRb0427, regulates worm behavior: worms learn to avoid this pathogenic bacterium following exposure, and this learned avoidance is inherited for four generations. The learned response is entirely mediated by bacterially-produced small RNAs, which induce avoidance and transgenerational inheritance, providing further support that such mechanisms of learning and inheritance exist in the wild. We identified Pv1, a small RNA expressed in P. vranovensis, that has a 16-nucleotide match to an exon of the C. elegans gene maco-1. Pv1 is both necessary and sufficient to induce learned avoidance of Grb0427. However, Pv1 also results in avoidance of a beneficial microbiome strain, P. mendocina. Our findings suggest that bacterial small RNA-mediated regulation of host behavior and its transgenerational inheritance may be functional in C. elegans' natural environment, and that this potentially maladaptive response may favor reversal of the transgenerational memory after a few generations. Our data also suggest that different bacterial small RNA-mediated regulation systems evolved independently, but define shared molecular features of bacterial small RNAs that produce transgenerationally-inherited effects.
Topics: Animals; Humans; Caenorhabditis elegans; Caenorhabditis elegans Proteins; RNA, Small Interfering; RNA Interference; RNA, Bacterial; Pseudomonas aeruginosa; Bacteria
PubMed: 38547071
DOI: 10.1371/journal.pgen.1011178 -
MSystems Apr 2024Plant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N...
Plant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N metabolism in plant microbiomes is largely limited. Here we examined the assembly and temporal dynamics of diazotrophic communities across multiple compartments (soils, epiphytic and endophytic niches of root and leaf, and grain) of three cereal crops (maize, wheat, and barley) and identified the potential N-cycling pathways in phylloplane microbiomes. Our results demonstrated that the microbial species pool, influenced by site-specific environmental factors (e.g., edaphic factors), had a stronger effect than host selection (i.e., plant species and developmental stage) in shaping diazotrophic communities across the soil-plant continuum. Crop diazotrophic communities were dominated by a few taxa (~0.7% of diazotrophic phylotypes) which were mainly affiliated with , , , and . Furthermore, eight dominant taxa belonging to and were identified as keystone diazotrophic taxa for three crops and were potentially associated with microbial network stability and crop yields. Metagenomic binning recovered 58 metagenome-assembled genomes (MAGs) from the phylloplane, and the majority of them were identified as novel species (37 MAGs) and harbored genes potentially related to multiple N metabolism processes (e.g., nitrate reduction). Notably, for the first time, a high-quality MAG harboring genes involved in the complete denitrification process was recovered in the phylloplane and showed high identity to . Overall, these findings significantly expand our understanding of ecological drivers of crop diazotrophs and provide new insights into the potential microbial N metabolism in the phyllosphere.IMPORTANCEPlants harbor diverse nitrogen-fixing microorganisms (i.e., diazotrophic communities) in both belowground and aboveground tissues, which play a vital role in plant nitrogen supply and growth promotion. Understanding the assembly and temporal dynamics of crop diazotrophic communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the site-specific microbial species pool largely shapes the structure of diazotrophic communities in the leaves and roots of three cereal crops. We further identify keystone diazotrophic taxa in crop microbiomes and characterize potential microbial N metabolism pathways in the phyllosphere, which provides essential information for developing microbiome-based tools in future sustainable agricultural production.
Topics: Microbiota; Agriculture; Soil; Nitrogen; Crops, Agricultural; Plant Development
PubMed: 38501864
DOI: 10.1128/msystems.01055-23 -
Molecular Biology Reports Mar 2024A novel lytic bacteriophage (phage) was isolated with Pseudomonas mendocina strain STP12 (P. mendocina) from the untreated site of Sewage Treatment Plant of Lovely...
BACKGROUND
A novel lytic bacteriophage (phage) was isolated with Pseudomonas mendocina strain STP12 (P. mendocina) from the untreated site of Sewage Treatment Plant of Lovely Professional University, India. P. mendocina is a Gram-negative, rod-shaped, aerobic bacterium belonging to the family Pseudomonadaceae and has been reported in fifteen (15) cases of economically important diseases worldwide.
METHODS AND RESULTS
Here, a novel phage specifically infecting and killing P. mendocina strain STP12 was isolated from sewage sample using enrichment, spot test and double agar overlay (DAOL) method and was designated as vB_PmeS_STP12. The phage vB-PmeS-STP12 was viable at wide range of pH and temperature ranging from 4 to10 and - 20 to 70 °C respectively. Host range and efficiency of plating (EOP) analysis indicated that phage vB-PmeS-STP12 was capable of infecting and killing P. mendocina strain STP6 with EOP of 0.34. Phage vB_PmeS_STP12 was found to have a significant bacterial reduction (p < 0.005) at all the doses administered, particularly at optimal MOI of 1 PFU/CFU, compared to the control. Morphological analysis using high resolution transmission electron microscopy (HR-TEM) revealed an icosahedral capsid of ~ 55 nm in diameter on average with a short, non-contractile tail. The genome of vB_PmeS_STP12 is a linear, dsDNA containing 36,212 bp in size with a GC content of 58.87% harbouring 46 open reading frames (ORFs). The 46 predicted ORFs encode proteins with functional information categorized as lysis, replication, packaging, regulation, assembly, infection, immune, and hypothetical. However, the genome of vB_PmeS_STP12 appeared to be devoid of tRNAs, integrase gene, toxins genes, virulence factors, antimicrobial resistance genes (ARGs) and CRISPR arrays. The blast analysis with phylogeny revealed that vB_PmeS_STP12 is genetically similar to Pseudomonas phage PMBT14, Pseudomonas phage Almagne and Serratia phage Serbin with a highest identity of 74.00%, 74.93% and 59.48% respectively.
CONCLUSIONS
Taken together, characterization, morphological analysis and genome-informatics indicated that vB_PmeS_STP12 is podovirus morphotype belonging to the class Caudoviticetes, family Zobellviridae which appeared to be devoid of integrase gene, ARGs, CRISPR arrays, virulence factors and toxins genes, exhibiting stability and infectivity at wide range of pH (4 to10) and temperature (-20 to 70 °C), thereby making vB_PmeS_STP12 suitable for phage therapy or biocontrol. Based on the bibliometric analysis and data availability with respect to sequences deposited in GenBank, this is the first report of a phage infecting Pseudomonas mendocina.
Topics: Humans; Bacteriophages; Pseudomonas; Phage Therapy; Sewage; Genome, Viral; Informatics; Integrases; Virulence Factors; Phylogeny
PubMed: 38483683
DOI: 10.1007/s11033-024-09362-3 -
Microorganisms Nov 2023Siderophores are low-molecular-weight and high-affinity molecules produced by bacteria under iron-limited conditions. Due to the low iron (III) (Fe) levels in surface...
Siderophores are low-molecular-weight and high-affinity molecules produced by bacteria under iron-limited conditions. Due to the low iron (III) (Fe) levels in surface waters in the marine environment, microbes produce a variety of siderophores. In the current study, halophilic bacteria SMI_1, sp., AABM_9, and AMPPS_5 were isolated from marine surface water of Kalinga beach, Bay of Bengal (Visakhapatnam, Andhra Pradesh, India) and were investigated for siderophore production using the Chrome Azurol S (CAS) assay. The effect of various production parameters was also studied. The optimum production of siderophores for SMI_1 was 93.57% siderophore units (SU) (after 48 h of incubation at 30 °C, pH 8, sucrose as carbon source, sodium nitrate as nitrogen source, 0.4% succinic acid), and for AABM_9, it was 87.18 %SU (after 36 h of incubation period at 30 °C, pH 8, in the presence of sucrose, ammonium sulfate, 0.4% succinic acid). The maximum production of siderophores for AMPPS_5 was 91.17 %SU (after 36 h of incubation at 35 °C, pH 8.5, glucose, ammonium sulfate, 0.4% citric acid). The bacterial isolates SMI_1, AABM_9, and AMPPS_5 showed siderophore production at low Fe concentrations of 0.10 µM, 0.01 µM, and 0.01 µM, respectively. The SMI_1 (73.09 %SU) and AMPPS_5 (68.26 %SU) isolates showed siderophore production in the presence of Zn (10 µM), whereas AABM_9 (50.4 %SU) exhibited siderophore production in the presence of Cu (10 µM). Additionally, these bacterial isolates showed better heavy-metal chelation ability and rapid development in seed germination experiments. Based on these results, the isolates of marine-derived bacteria effectively produced the maximum amount of siderophores, which could be employed in a variety of industrial and environmental applications.
PubMed: 38138017
DOI: 10.3390/microorganisms11122873 -
Bioresource Technology Feb 2024A salt-tolerant strain, Pseudomonas mendocina A4, was isolated from brackish-water ponds showing simultaneous heterotrophic nitrification-aerobic denitrification and...
Simultaneous aerobic nitrogen and phosphate removal capability of novel salt-tolerant strain, Pseudomonas mendocina A4: Characterization, mechanism and application potential.
A salt-tolerant strain, Pseudomonas mendocina A4, was isolated from brackish-water ponds showing simultaneous heterotrophic nitrification-aerobic denitrification and phosphorus removal capability. The optimal conditions for nitrogen and phosphate removal of strain A4 were pH 7-8, carbon/nitrogen ratio 10, phosphorus/nitrogen ratio 0.2, temperature 30 °C, and salinity range of 0-5 % using sodium succinate as the carbon source. The nitrogen and phosphate removal efficiencies were 96-100 % and 88-96 % within 24 h, respectively. The nitrogen and phosphate removal processes were matched with the modified Gompertz model, and the underlying mechanisms were confirmed by the activities of key metabolic enzymes. Under 10 % salinity, the immobilization technology was employed to enhance the nitrogen and phosphate removal efficiencies of strain A4, achieving 87 % and 76 %, respectively. These findings highlight the potential application of strain A4 in both freshwater and marine culture wastewater treatment.
Topics: Denitrification; Phosphates; Pseudomonas mendocina; Nitrogen; Aerobiosis; Nitrification; Phosphorus; Heterotrophic Processes; Carbon; Nitrites; Nitrogen Radioisotopes
PubMed: 37989421
DOI: 10.1016/j.biortech.2023.130047 -
Bioresource Technology Jan 2024Bio-mitigation of plastics by microorganisms generates carbon dioxide (CO) that can be utilized for algal biomass generation. Pseudomonas mendocina ABF786, reportedly...
Bio-mitigation of plastics by microorganisms generates carbon dioxide (CO) that can be utilized for algal biomass generation. Pseudomonas mendocina ABF786, reportedly the most efficient plastic-degrading bacteria, was screened using the modified most probable number technique. This study highlights the use of an integrative prototype for the production of microalgal biomass (Chlorella vulgaris) in combination with bio-mitigation of plastics, which serves a dual purpose: (i) increased plastic-degradation capability by microorganisms (53%-85% increase in plastic weight loss) due to removal of CO feedback inhibition and (ii) increased algal biomass generation (200%-237%) due to supply of extra CO from plastic degradation to the algal cultivation flask. Whole-genome sequencing and functional annotation confirmed that all the genes involved in the mineralization of plastic to CO are present within the genome of P. mendocina ABF786. Using two or more microbial cultures for remediation may increase the process efficiency.
Topics: Chlorella vulgaris; Biofuels; Carbon Dioxide; Pseudomonas mendocina; Microalgae; Biomass
PubMed: 37925087
DOI: 10.1016/j.biortech.2023.129952 -
Foodborne Pathogens and Disease Nov 2023The purpose of this research was to analyze the functional portraits and genomic features of carbapenem-resistant carrying and . The resistance mechanism of the strain...
The purpose of this research was to analyze the functional portraits and genomic features of carbapenem-resistant carrying and . The resistance mechanism of the strain was verified by experiments. Genomic data were aligned and analyzed in the NCBI database. Growth curve measurements were used to describe the growth characteristics of the bacteria. The virulence of strain was analyzed by serum killing assay and biofilm formation assay. Plasmid conjugation experiments were performed to verify the transferability of plasmids carrying drug-resistance genes. The strain was highly resistant to carbapenems. In addition, ST typing is unknown and has been submitted to Genebank. The strain carried two carbapenemase genes, including and . Among them, was located on a 5.62832 Mb chromosome, and was located on a 172.851 Kb transferable plasmid, which was a very close relative of pIMP-NY7610 in China. The strain also had a variety of virulence genes, which were expressed in the siderophore, capsule, pilus, alginate, flagella, etc. The study suggests that the functional portrait and genomic features of carbapenem-resistant harboring and are unique to China. This outcome represents antibiotic resistance exhibited in the genus by acquiring chromosomes and plasmid genes. The monitoring and supervision of antimicrobial usage must be strengthened since the multi-drug-resistant and moderately virulent will attract much attention in the near future.
Topics: Carbapenems; Pseudomonas mendocina; beta-Lactamases; Plasmids; Drug Resistance, Microbial; Microbial Sensitivity Tests; Genomics; China; Anti-Bacterial Agents
PubMed: 37729068
DOI: 10.1089/fpd.2023.0055 -
Toxics Jul 2023Phytoremediation can help remediate potential toxic elements (PTE) in soil. Microorganisms and soil amendments are effective means to improve the efficiency of...
Phytoremediation can help remediate potential toxic elements (PTE) in soil. Microorganisms and soil amendments are effective means to improve the efficiency of phytoremediation. This study selected three microorganisms that may promote phytoremediation, including bacteria (), fungi (), and arbuscular-mycorrhizal fungi (AMF, ). The effects of single or mixed inoculation of three microorganisms on the phytoremediation efficiency of and were tested under three different degrees of cadmium-contaminated soil (low 10 mg/kg, medium 50 mg/kg, and high 100 mg/kg). The results showed that single inoculation of AMF or could significantly increase the biomass of two plants under three different degrees of cadmium-contaminated soil, and the growth-promoting effect of AMF was better than . However, simultaneous inoculation of these two microorganisms did not show a better effect than the inoculation of one. Inoculation of reduced the biomass of the two plants under high concentrations of cadmium-contaminated soil. Among all treatments, the remediation ability of the two plants was the strongest when inoculated with AMF alone. On this basis, this study explored the effect of AMF combined with corn-straw-biochar on the phytoremediation efficiency of and . The results showed that biochar could affect plant biomass and Cd concentration in plants by reducing Cd concentration in soil. The combined use of biochar and AMF increased the biomass of by 8.9-48.6% and the biomass of by 8.04-32.92%. Compared with the single use of AMF or biochar, the combination of the two is better, which greatly improves the efficiency of phytoremediation.
PubMed: 37505548
DOI: 10.3390/toxics11070582